Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
GenotypeGVCFs reporting every site to have MQ0=0
In the past, I’ve found MQ0 ("Total Mapping Quality Zero Reads") to be a very useful INFO feature of putatively variable sites. However, in my experience, GenotypeGVCFs reports every site to have MQ0=0, even those for which UnifiedGenotyper reports MQ0 > 0 when run on the same data. Is this a bug, or am I missing something?